Geomorph Version 2.0 Now Available!

April 16, 2014
By

(This article was first published on geomorph, and kindly contributed to R-bloggers)

Geomorph users,

We have uploaded version 2.0 to CRAN. The windows and mac binaries have been compiled and the tarball is available.

Version 2.0 comes with substantial changes and new features: 

New function phylo.pls()for assessing the multivariate association between two blocks of variables in a phylogenetic context. This is based on a new paper by Adams and Felice

New function two.b.pls() for assessing the multivariate association between two blocks of variables

New function morphol.disparity() to compare Procrustes variance disparity among groups

New method for function physignal() to calculate phylogenetic signal using a generalized Kappa statsitic. This is based on a new paper by Adams (Systematic Biology in press)

F-ratios and R-squared values added to output of ProcD.lm()

3D Visualizations now include "surface" option to view shape deformation as warped mesh3d surfaces in the following: plotRefToTarget(), plotTangentSpace(), plotAllometry(), and bilat.symmetry(). 

New I/O functions: warpRefMesh() to create a mesh3d surface that represents the mean shape, findMeanSpec() to assist in choosing a template ply file for use with warpRefMesh() that identifies specimen closest to the mean shape, and defline.modules() to interactively assign landmarks to modular partitions (currently 2D only)

Generalized data input to allow 3D array or 2D matrix of data added to the following analysis functions: compare.evol.rates(), phylo.pls(), morphol.integr(), two.b.pls(), physignal(), and plotGMPhyloMorphoSpace()

Ability to input univariate data added to compare.evol.rates() and physignal()


Verbose output = T/F added to the following functions: bilat.symmetry(), phylo.pls(), two.b.pls(), morphol.integr(), plotAllometry(), plotTangentSpace(), physignal(). This new option allows the user to decide what information should be returned. Verbose=F, the default, returns the basic output, usually the test statistic and P-value.Verbose=T, returns new datasets, shape scores and more. 

As always, all the changes and additions for this version can be found in the geomorph news file.

Emma




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